shapeFeatures

Radiomics shape features

Since R2023b

Syntax

S = shapeFeatures(R)

S = shapeFeatures(R,Name=Value)

Description

S = shapeFeatures(R) computes the radiomics shape features S for the radiomics object R.

S = shapeFeatures(R,Name=Value) specifies additional options using one or more optional name-value arguments.

Examples

Compute Shape Features for Multiple ROIs in 2-D X-Ray Image

Load an X-ray image into the workspace as a medicalImage object. Visualize the image.

data = medicalImage("forearmXrayImage1.dcm");
I = data.Pixels;
figure
imshow(I,[])

Draw two regions of interest (ROI) in the X-ray image. Create masks from the ROIs.

roi1 = drawassisted(Color="g");
roi2 = drawassisted(Color="r");

mask1 = createMask(roi1,I);
mask2 = createMask(roi2,I);

Create an ROI label matrix, using different labels for the two ROIs. Create a medicalImage object of the ROI label data.

mask = zeros(size(I));
mask(mask1) = 1;
mask(mask2) = 2;
info = dicominfo("forearmXrayImage1.dcm");
roi = medicalImage(mask,info);

Create a radiomics object from the X-ray image data and ROI label data.

R = radiomics(data,roi)

R = 
  radiomics with properties:

                             Data: [1×1 medicalImage]
                         ROILabel: [1×1 medicalImage]
                         Resample: 0
                        Resegment: 1
                       Discretize: 1
                    DiscretizeIVH: 1
            ResampledVoxelSpacing: []
               DataResampleMethod: []
               MaskResampleMethod: []
              ResegmentationRange: []
                  ExcludeOutliers: 1
       DiscreteBinSizeOrBinNumber: []
                   DiscreteMethod: 'FixedBinNumber'
    DiscreteIVHBinSizeOrBinNumber: []
                DiscreteIVHMethod: 'FixedBinNumber'

Compute shape features for both ROIs.

S = shapeFeatures(R)

S=2×24 table
    LabelID    VolumeMesh2D    VolumeVoxelCount2D    SurfaceAreaMesh2D    SurfaceVolumeRatio2D    Compactness1_2D    Compactness2_2D    SphericalDisproportion2D    Sphericity2D    Asphericity2D    CentreOfMassShift2D    Maximum3dDiameter2D    MajorAxisLength2D    MinorAxisLength2D    LeastAxisLength2D    Elongation2D    Flatness2D    VolumeDensityAABB_2D    AreaDensityAABB_2D    VolumeDensityAEE_2D    AreaDensityAEE_2D    VolumeDensityConvexHull2D    AreaDensityConvexHull2D    IntegratedIntensity2D
    _______    ____________    __________________    _________________    ____________________    _______________    _______________    ________________________    ____________    _____________    ___________________    ___________________    _________________    _________________    _________________    ____________    __________    ____________________    __________________    ___________________    _________________    _________________________    _______________________    _____________________

      "1"           54               54.427               135.84                 2.5156              0.019243            0.13156                 1.9662                0.5086          0.96618             0.18567                11.327                10.188                6.924                  0              0.67962           0               0.63176                0.65158                  NaN                 0.91886                  0.98182                     0.99044                 1.2498e+05      
      "2"           74                74.85                181.6                  2.454              0.017061            0.10342                 2.1304               0.46939           1.1304             0.24847                11.563                11.187               8.7535                  0              0.78246           0               0.64598                0.66783                  NaN                 0.83862                  0.93671                      0.9552                 1.8045e+05      

Compute Shape Features for 3-D Computed Tomography (CT) Image

Import a computed tomography (CT) image volume and the corresponding ROI mask volume from the IBSI validation data set [1][2][3] as medicalVolume objects.

unzip("CTImageMaskNIfTI.zip")
data = medicalVolume("CT_image.nii.gz");
roi = medicalVolume("CT_mask.nii.gz");

Visualize a slice of the CT image volume and the corresponding ROI.

figure
imshowpair(data.Voxels(:,:,20),roi.Voxels(:,:,20),"montage")

Create a radiomics object, using the CT image volume and ROI mask volume, with default preprocessing options.

R = radiomics(data,roi)

R = 
  radiomics with properties:

                             Data: [1×1 medicalVolume]
                         ROILabel: [1×1 medicalVolume]
                         Resample: 1
                        Resegment: 1
                       Discretize: 1
                    DiscretizeIVH: 1
            ResampledVoxelSpacing: 1
               DataResampleMethod: 'linear'
               MaskResampleMethod: 'linear'
              ResegmentationRange: []
                  ExcludeOutliers: 1
       DiscreteBinSizeOrBinNumber: []
                   DiscreteMethod: 'FixedBinNumber'
    DiscreteIVHBinSizeOrBinNumber: []
                DiscreteIVHMethod: 'FixedBinNumber'

Compute the shape features of the ROI in both the 2-D resampled and 3-D resampled CT image volumes.

S = shapeFeatures(R,Type="all",SubType="all")

S=1×51 table
    LabelID    VolumeMesh2D    VolumeVoxelCount2D    SurfaceAreaMesh2D    SurfaceVolumeRatio2D    Compactness1_2D    Compactness2_2D    SphericalDisproportion2D    Sphericity2D    Asphericity2D    CentreOfMassShift2D    Maximum3dDiameter2D    MajorAxisLength2D    MinorAxisLength2D    LeastAxisLength2D    Elongation2D    Flatness2D    VolumeDensityAABB_2D    AreaDensityAABB_2D    VolumeDensityAEE_2D    AreaDensityAEE_2D    VolumeDensityConvexHull2D    AreaDensityConvexHull2D    IntegratedIntensity2D    MoransIIndex2D    GearysCMeasure2D    VolumeMesh3D    VolumeVoxelCount3D    SurfaceAreaMesh3D    SurfaceVolumeRatio3D    Compactness1_3D    Compactness2_3D    SphericalDisproportion3D    Sphericity3D    Asphericity3D    CentreOfMassShift3D    Maximum3dDiameter3D    MajorAxisLength3D    MinorAxisLength3D    LeastAxisLength3D    Elongation3D    Flatness3D    VolumeDensityAABB_3D    AreaDensityAABB_3D    VolumeDensityAEE_3D    AreaDensityAEE_3D    VolumeDensityConvexHull3D    AreaDensityConvexHull3D    IntegratedIntensity3D    MoransIIndex3D    GearysCMeasure3D
    _______    ____________    __________________    _________________    ____________________    _______________    _______________    ________________________    ____________    _____________    ___________________    ___________________    _________________    _________________    _________________    ____________    __________    ____________________    __________________    ___________________    _________________    _________________________    _______________________    _____________________    ______________    ________________    ____________    __________________    _________________    ____________________    _______________    _______________    ________________________    ____________    _____________    ___________________    ___________________    _________________    _________________    _________________    ____________    __________    ____________________    __________________    ___________________    _________________    _________________________    _______________________    _____________________    ______________    ________________

      "1"         52504              52637                8411.4                 0.1602              0.038399            0.52389                 1.2405               0.80615          0.24047             0.91477                56.989                50.304                 44                 33.402            0.87467         0.664             0.47158                0.59688                1.3563                1.4179                   0.90243                     1.1059                  3.1173e+06             0.013525           0.97867            52923              52975                 8425                 0.15919              0.038611            0.5297                  1.2359               0.80911          0.23592             0.8888                 57.359                50.405                44.1                33.518             0.8749        0.66497            0.46924                0.59248                1.3566                1.4135                   0.89714                     1.0994                  3.1069e+06             0.016362           0.96493     

[1] Vallières, Martin, Carolyn R. Freeman, Sonia R. Skamene, and Issam El Naqa. “A Radiomics Model from Joint FDG-PET and MRI Texture Features for the Prediction of Lung Metastases in Soft-Tissue Sarcomas of the Extremities.” The Cancer Imaging Archive, 2015. https://doi.org/10.7937/K9/TCIA.2015.7GO2GSKS.

[2] Vallières, M, C R Freeman, S R Skamene, and I El Naqa. “A Radiomics Model from Joint FDG-PET and MRI Texture Features for the Prediction of Lung Metastases in Soft-Tissue Sarcomas of the Extremities.” Physics in Medicine and Biology 60, no. 14 (July 7, 2015): 5471–96. https://doi.org/10.1088/0031-9155/60/14/5471.

[3] Clark, Kenneth, Bruce Vendt, Kirk Smith, John Freymann, Justin Kirby, Paul Koppel, Stephen Moore, et al. “The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository.” Journal of Digital Imaging 26, no. 6 (December 2013): 1045–57. https://doi.org/10.1007/s10278-013-9622-7.

Input Arguments

R — Data and ROI for feature computation

radiomics object

Data and ROI for feature computation, specified as a radiomics object. The radiomics object R contains details of the preprocessed data and region of interest (ROI) from which to compute the features.

Name-Value Arguments

Specify optional pairs of arguments as Name1=Value1,...,NameN=ValueN, where Name is the argument name and Value is the corresponding value. Name-value arguments must appear after other arguments, but the order of the pairs does not matter.

Example: shapeFeatures(R,SubType="2D") computes the shape features on 2-D resampled data.

Type — Category of shape features

"basic" (default) | "all"

Category of shape features to compute, specified as one of these options.

• "basic"

• "all"

If you specify "all", the function computes advanced features in addition to basic features. For more information on which specific shape features each category includes, see IBSI Standard and Radiomics Function Feature Correspondences.

Data Types: char | string

SubType — Resampling from which to compute shape features

"2D" | "3D" | "all"

Resampling from which to compute shape features, specified as one of these options.

• "2D" — Computes features from the 2-D resampled data. This is the default option for 2-D data, when the Data and ROILabel properties of the radiomics object R are 2-D matrices or medicalImage objects.

• "3D" — Computes features from the 3-D resampled data. This is the default option for 3-D data, when the Data and ROILabel properties of the radiomics object R are 3-D arrays or medicalVolume objects. 3-D resampling is not applicable for 2-D data.

• "all" — Computes features for all applicable options.

For 3-D data, when you perform 3-D resampling of the volume, the function makes the voxel spacing along all three spatial dimensions isotropic. However, when you perform 2-D resampling of the volume, the function makes the voxel spacing along only the x- and y-dimensions isotropic, while retaining the voxel spacing of the input volume along the z-dimension.

Data Types: char | string

Output Arguments

S — Shape features

table

Shape features, returned as a table. The first column in S is LabelID. The subsequent columns are the shape features. Each row of the table corresponds to an ROI. For more details on which shape features are computed in each Type and SubType, see IBSI Standard and Radiomics Function Feature Correspondences.

Version History

Introduced in R2023b

R2025a: Compute shape features for multiple ROIs

Compute shape features for multiple regions of interest (ROIs) in a medical image or medical volume.

R2024b: Compute new shape features, specify type of shape features

Compute two new shape features, MoransIIndex and GearyCMeasure, in the region of interest of a medical volume. Specify whether you want to compute basic shape features or all shape features using the new name-value argument Type.

R2024a: Compute new shape features in radiomics analysis

Compute two new shape features, maximum3dDiameter and AreaDensityAEE, in the region of interest of a medical volume.